bims-nenemi 2024-12-01 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2024–12–01
seventeen papers selected by
Marco Tigano, Thomas Jefferson University

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging.
DNA sequence and lesion-dependent mitochondrial transcription factor A (TFAM)-DNA-binding modulates DNA repair activities and products.
Unveiling a novel signalling pathway involving NRF2 and PGAM5 in regulating the mitochondrial unfolded protein response in stressed cardiomyocytes.
ER-tethered stress sensor CREBH regulates mitochondrial unfolded protein response to maintain energy homeostasis.
Analysis of mitochondrial DNA replisome in autism spectrum disorder: Exploring the role of replisome genes.
Mitochondria-localized MBD2c facilitates mtDNA transcription and drug resistance.
The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo.
Stimulated Emission Depletion Imaging Reveals Mitochondrial Phenotypic Heterogeneity under Apoptosis Stimuli across Living Glioma Models.
Impaired proteasome induces mitochondrial DNA release to activate the cGAS-STING signaling pathway and cause necroptosis in mouse brain.
Apoptotic Caspases Suppress Expression of Endogenous Retroviruses in HPV31+ Cells That Are Associated with Activation of an Innate Immune Response.
Mutations in mitochondrial ATAD3 gene and disease, lessons from in vivo models.
Deep learning-enhanced automated mitochondrial segmentation in FIB-SEM images using an entropy-weighted ensemble approach.
Quantification of subcellular RNA localization through direct detection of RNA oxidation.
Piezo1 exacerbates inflammation-induced cartilaginous endplate degeneration by activating mitochondrial fission via the Ca2+/CaMKII/Drp1 axis.
Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Neuroglobin-enriched secretome provides neuroprotection against hydrogen peroxide and mitochondrial toxin-induced cellular stress.
Structure and function of the human mitochondrial MRS2 channel.

Genome Res. 2024 Nov 27. pii: gr.279072.124. [Epub ahead of print]

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging.

Amy R Vandiver, Allen Herbst, Paul Stothard, Jonathan Wanagat.

While it is well understood that mitochondrial DNA (mtDNA) deletion mutations cause incurable diseases and contribute to aging, little is known about the transcriptional products that arise from these DNA structural variants. We hypothesized that mitochondrial genomes containing deletion mutations express chimeric mitochondrial RNAs. To test this, we analyzed human and rat RNA sequencing data to identify, quantitate, and characterize chimeric mitochondrial RNAs. We observed increased chimeric mitochondrial RNA frequency in samples from patients with mitochondrial genetic diseases and in samples from aged humans. The spectrum of chimeric mitochondrial transcripts reflected the known pattern of mtDNA deletion mutations. To test the hypothesis that mtDNA deletions induce chimeric RNA transcripts, we treated 18 mo and 34 mo rats with guanidinopropionic acid to induce high levels of skeletal muscle mtDNA deletion mutations. With mtDNA deletion induction, we demonstrate that the chimeric mitochondrial transcript frequency also increased and correlated strongly with an orthogonal DNA-based mutation assay performed on identical samples. Further, we show that the frequency of chimeric mitochondrial transcripts predicts expression of both nuclear and mitochondrial genes central to mitochondrial function, demonstrating the utility of these events as metrics of age-induced metabolic change. Mapping and quantitation of chimeric mitochondrial RNAs provides an accessible, orthogonal approach to DNA-based mutation assays, offers a potential method for identifying mitochondrial pathology in widely accessible datasets, and opens a new area of study in mitochondrial genetics and transcriptomics.

DOI: https://doi.org/10.1101/gr.279072.124
Nucleic Acids Res. 2024 Nov 28. pii: gkae1144. [Epub ahead of print]

DNA sequence and lesion-dependent mitochondrial transcription factor A (TFAM)-DNA-binding modulates DNA repair activities and products.

Kathleen Urrutia, Yu Hsuan Chen, Jin Tang, Ta I Hung, Guodong Zhang, Wenyan Xu, Wenxin Zhao, Dylan Tonthat, Chia-En A Chang, Linlin Zhao.

Mitochondrial DNA (mtDNA) is indispensable for mitochondrial function and is maintained by DNA repair, turnover, mitochondrial dynamics and mitophagy, along with the inherent redundancy of mtDNA. Base excision repair (BER) is a major DNA repair mechanism in mammalian mitochondria. Mitochondrial BER enzymes are implicated in mtDNA-mediated immune response and inflammation. mtDNA is organized into mitochondrial nucleoids by mitochondrial transcription factor A (TFAM). The regulation of DNA repair activities by TFAM-DNA interactions remains understudied. Here, we demonstrate the modulation of DNA repair enzymes by TFAM concentrations, DNA sequences and DNA modifications. Unlike previously reported inhibitory effects, we observed that human uracil-DNA glycosylase 1 (UNG1) and AP endonuclease I (APE1) have optimal activities at specific TFAM/DNA molar ratios. High TFAM/DNA ratios inhibited other enzymes, OGG1 and AAG. In addition, TFAM reduces the accumulation of certain repair intermediates. Molecular dynamics simulations and DNA-binding experiments demonstrate that the presence of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in certain sequence motifs enhances TFAM-DNA binding, partially explaining the inhibition of OGG1 activity. Bioinformatic analysis of published 8-oxodG, dU, and TFAM-footprint maps reveals a correlation between 8-oxodG and TFAM locations in mtDNA. Collectively, these results highlight the complex regulation of mtDNA repair by DNA sequence, TFAM concentrations, lesions and repair enzymes.

DOI: https://doi.org/10.1093/nar/gkae1144
Int J Biochem Cell Biol. 2024 Nov 26. pii: S1357-2725(24)00197-3. [Epub ahead of print] 106704

Unveiling a novel signalling pathway involving NRF2 and PGAM5 in regulating the mitochondrial unfolded protein response in stressed cardiomyocytes.

Rahme Nese Safakli, Stephen Gray, Nadia Bernardi, Ioannis Smyrnias.

  The mitochondrial unfolded protein response (UPRmt) is a conserved signalling pathway that initiates a specific transcriptional programme to maintain mitochondrial and cellular homeostasis under stress. Previous studies have demonstrated that UPRmt activation has protective effects in the pressure-overloaded human heart, suggesting that robust UPRmt stimulation could serve as an intervention strategy for cardiovascular diseases. However, the precise mechanisms of UPRmt regulation remain unclear. In this study, we present evidence that the NRF2 transcription factor is involved in UPRmt activation in cardiomyocytes during conditions of mitochondrial stress. Silencing NRF2 partially reduces UPRmt activation, highlighting its essential role in this pathway. However, constitutive activation of NRF2 via inhibition of its cytosolic regulator KEAP1 does not increase levels of UPRmt activation markers, suggesting an alternative regulatory mechanism independent of the canonical KEAP1-NRF2 axis. Further analysis revealed that NRF2 likely affects UPRmt activation through its interaction with PGAM5 at the mitochondrial membrane. Disruption of PGAM5 in cardiomyocytes subjected to mitochondrial stress reduces the interaction between PGAM5 and NRF2, enhancing nuclear translocation of NRF2 and significantly upregulating the UPRmt in an NRF2-dependent manner. This NRF2-regulated UPRmt amplification improves mitochondrial respiration, reflecting an enhanced capacity for cardiomyocytes to meet elevated energetic demands during mitochondrial stress. Our findings highlight the therapeutic potential of targeting the NRF2-PGAM5-KEAP1 signalling complex to amplify the UPRmt in cardiomyocytes for cardiovascular and other diseases associated with mitochondrial dysfunction. Future studies should aim to elucidate the mechanisms via which NRF2 enhances the protective effects of UPRmt, thereby contributing to more targeted therapeutic approaches.

Keywords:  cardiomyocytes; cardioprotection; mitochondria; stress; unfolded protein response

DOI:  https://doi.org/10.1016/j.biocel.2024.106704
Proc Natl Acad Sci U S A. 2024 Dec 03. 121(49): e2410486121

ER-tethered stress sensor CREBH regulates mitochondrial unfolded protein response to maintain energy homeostasis.

Hyunbae Kim, Qi Chen, Donghong Ju, Neeraja Purandare, Xuequn Chen, Lobelia Samavati, Li Li, Ren Zhang, Lawrence I Grossman, Kezhong Zhang.

  The Mitochondrial Unfolded Protein Response (UPRmt), a mitochondria-originated stress response to altered mitochondrial proteostasis, plays important roles in various pathophysiological processes. In this study, we revealed that the endoplasmic reticulum (ER)-tethered stress sensor CREBH regulates UPRmt to maintain mitochondrial homeostasis and function in the liver. CREBH is enriched in and required for hepatic Mitochondria-Associated Membrane (MAM) expansion induced by energy demands. Under a fasting challenge or during the circadian cycle, CREBH is activated to promote expression of the genes encoding the key enzymes, chaperones, and regulators of UPRmt in the liver. Activated CREBH, cooperating with peroxisome proliferator-activated receptor α (PPARα), activates expression of Activating Transcription Factor (ATF) 5 and ATF4, two major UPRmt transcriptional regulators, independent of the ER-originated UPR (UPRER) pathways. Hepatic CREBH deficiency leads to accumulation of mitochondrial unfolded proteins, decreased mitochondrial membrane potential, and elevated cellular redox state. Dysregulation of mitochondrial function caused by CREBH deficiency coincides with increased hepatic mitochondrial oxidative phosphorylation (OXPHOS) but decreased glycolysis. CREBH knockout mice display defects in fatty acid oxidation and increased reliance on carbohydrate oxidation for energy production. In summary, our studies uncover that hepatic UPRmt is activated through CREBH under physiological challenges, highlighting a molecular link between ER and mitochondria in maintaining mitochondrial proteostasis and energy homeostasis under stress conditions.

Keywords:  ER-mitochondria contact; cell metabolism; michondrial UPR; transcriptional regulation; unfolded protein response

DOI:  https://doi.org/10.1073/pnas.2410486121
Autism Res. 2024 Nov 29.

Analysis of mitochondrial DNA replisome in autism spectrum disorder: Exploring the role of replisome genes.

Valentina Rojas, Carlos Carrasco-Gallardo, Lidia Tenorio, Margrethe A Olesen, Victor Tapia, Manuel Carrasco, Patricio Araos, Rodrigo A Quintanilla, Lina M Ruiz.

  Autism spectrum disorder (ASD) is a neurodevelopmental condition often associated with mitochondrial dysfunction, including increased mitochondrial DNA (mtDNA) copy number and impaired energy production. This study investigates the role of the mitochondrial replisome-specifically, the genes TFAM, TWNK, POLG, and TOP1MT-in mtDNA replication and its potential contribution to ASD pathophysiology. We analyzed samples from the oral mucosa of children with ASD and typically developing (TD) controls, assessing mtDNA copy number, gene expression, and protein levels. Our findings revealed a significant increase in mtDNA copy number in the oral mucosa of ASD children, along with partially deleted mtDNA molecules. However, there were no significant changes in the expression of TFAM, TWNK, POLG, or MT-TL1 genes between ASD and TD samples. Additionally, TFAM protein levels, including monomeric, dimeric, and trimeric forms, did not differ significantly. We also observed increased oxidative stress and inflammatory markers in the oral mucosa of ASD children, suggesting that mitochondrial alterations may be linked to inflammation and oxidative damage in ASD. To further investigate the functional impact of TFAM, we overexpressed it in human HEK293 cells and cortical neurons (CN1.4). TFAM overexpression led to increased mtDNA copy number, cell proliferation, and ATP production in HEK293 cells, but did not significantly alter mitochondrial gene expression, protein oxidation, or mtDNA integrity. In CN1.4 neurons, TFAM overexpression increased mitochondrial membrane potential and length, indicating potential changes in mitochondrial dynamics. Overall, our study suggests that while mtDNA alterations are present in ASD, they are not directly driven by changes in mitochondrial replisome gene expression. These findings highlight the complexity of mitochondrial dysfunction in ASD and suggest the need for further investigation into the underlying molecular mechanisms.

Keywords:  ASD; MT‐TL1; POLG; TFAM overexpression; TOPMT1; TWNK; autism; mitochondrial DNA; mtDNA replisome; TFAM

DOI:  https://doi.org/10.1002/aur.3277
Nat Chem Biol. 2024 Nov 28.

Mitochondria-localized MBD2c facilitates mtDNA transcription and drug resistance.

Yijie Hao, Zilong Zhou, Rui Liu, Shengqi Shen, Haiying Liu, Yingli Zhou, Yuchen Sun, Qiankun Mao, Tong Zhang, Shi-Ting Li, Zhaoji Liu, Yiyang Chu, Linchong Sun, Ping Gao, Huafeng Zhang.

Mitochondria contain a 16-kb double stranded DNA genome encoding 13 proteins essential for respiration, but the mechanisms regulating transcription and their potential role in cancer remain elusive. Although methyl-CpG-binding domain (MBD) proteins are essential for nuclear transcription, their role in mitochondrial DNA (mtDNA) transcription is unknown. Here we report that the MBD2c splicing variant translocates into mitochondria to mediate mtDNA transcription and increase mitochondrial respiration in triple-negative breast cancer (TNBC) cells. In particular, MBD2c binds the noncoding region in mtDNA and interacts with SIRT3, which in turn deacetylates and activates TFAM, a primary mitochondrial transcription factor, leading to enhanced mtDNA transcription. Furthermore, MBD2c recovered the decreased mitochondrial gene expression caused by the DNA synthesis inhibitor cisplatin, preserving mitochondrial respiration and consequently enhancing drug resistance and proliferation in TNBC cells. These data collectively demonstrate that MBD2c positively regulates mtDNA transcription, thus connecting epigenetic regulation by deacetylation with cancer cell metabolism, suggesting druggable targets to overcome resistance.

DOI: https://doi.org/10.1038/s41589-024-01776-1
Mol Cell. 2024 Nov 19. pii: S1097-2765(24)00884-0. [Epub ahead of print]

The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo.

Anna Constance Vind, Zhenzhen Wu, Muhammad Jasrie Firdaus, Goda Snieckute, Gee Ann Toh, Malin Jessen, José Francisco Martínez, Peter Haahr, Thomas Levin Andersen, Melanie Blasius, Li Fang Koh, Nina Loeth Maartensson, John E A Common, Mads Gyrd-Hansen, Franklin L Zhong, Simon Bekker-Jensen.

  Solar UVB light causes damage to the outermost layer of skin. This insult induces rapid local responses, such as dermal inflammation, keratinocyte cell death, and epidermal thickening, all of which have traditionally been associated with DNA damage response signaling. Another stress response that is activated by UVB light is the ribotoxic stress response (RSR), which depends on the ribosome-associated mitogen-activated protein 3 kinases (MAP3K) ZAKα and culminates in p38 and JNK activation. Using ZAK knockout mice, we here show that it is the RSR that is responsible for the early manifestation of UVB-induced skin inflammation and keratinocyte death and subsequent proliferation in vivo. We also show that the RSR controls both p38-mediated pyroptotic and JNK-mediated apoptotic programmed cell death of human keratinocytes in vitro. In sum, our work highlights that skin cells rely on a cytoplasmic and ribosomal stress signal rather than a nuclear and DNA-templated signal for rapid inflammatory responses to UV exposure.

Keywords:  JNK; UV; ZAK-alpha; apoptosis; inflammation; p38; pyroptosis; ribotoxic stress response; skin

DOI:  https://doi.org/10.1016/j.molcel.2024.10.044
Nano Lett. 2024 Nov 25.

Stimulated Emission Depletion Imaging Reveals Mitochondrial Phenotypic Heterogeneity under Apoptosis Stimuli across Living Glioma Models.

Lu Gao, Beibei Gao, Wei Ge, Shuxian Li, Fu Wang.

  The mitochondrial phenotypes contribute to the understanding of disease mechanisms and treatments, which are typically characterized through the omics methods. However, the high dynamics and phenotypic heterogeneity of mitochondria require high-resolution characterization within individual living cells. Therefore, we introduce a fluorescence analysis method, based on two-color and fluorescence lifetime stimulated emission depletion (STED) super-resolution imaging, to explore mitochondrial phenotypic heterogeneity in human (U87) and mouse (GL261) glioma models. Furthermore, we used rotenone and etoposide to simulate the effects of antitumor drugs, inducing apoptosis through mitochondrial dysfunction, respectively. The two-color labeling introduces intracellular parameters to qualitatively visualize changes in mitochondrial morphology, while fluorescence lifetime reflects the status of mitochondria and their microenvironment from the perspective of probe characteristics. This method reveals mitochondria phenotypic heterogeneity induced by the apoptotic stimuli in human and mouse glioma models from a morphological perspective.

Keywords:  STED imaging; apoptosis; glioma; heterogeneity; mitochondria phenotypes

DOI:  https://doi.org/10.1021/acs.nanolett.4c04986
bioRxiv. 2024 Nov 14. pii: 2024.11.13.623442. [Epub ahead of print]

Impaired proteasome induces mitochondrial DNA release to activate the cGAS-STING signaling pathway and cause necroptosis in mouse brain.

Abena Dwamena, Yasin Asadi, Erin Gilstrap, Hongmin Wang.

Impaired proteasome function is consistently associated with many neurodegenerative disorders, including Alzheimer's disease (AD), showing neuroinflammation and neurodegeneration; however, how impaired proteasome causes neuroinflammation and neuronal death remains less understood. Here, we studied the effect of impaired proteasome on neuroinflammation and neuronal death in a knockout (KO) mouse model with reduced proteasome activity in the brain. We discovered that impaired proteasome led to the release of mitochondrial dsDNA into the cytosol, activating the cGAS-STING signaling pathway, and upregulating pro-inflammatory cytokines in the KO mouse brain relative to the control brain. Importantly, we also observed reduced brain weight, elevation of the mixed lineage kinase domain-like (MLKL) protein, phosphorylated MLKL, and receptor-interactive protein kinases (RIPK) 1 and 3 in the KO mouse brain compared to the control brain, suggesting activation of necroptosis in the KO brains. These data indicate that impaired proteasome activates the cGAS-STING pathway to induce neuroinflammation and neurodegeneration via a necroptotic manner. Our results suggest that neuroinflammation and necroptosis may be generalized factors caused by reduced proteasome activity observed in diverse neurodegenerative disorders.

DOI: https://doi.org/10.1101/2024.11.13.623442
Viruses. 2024 Oct 30. pii: 1695. [Epub ahead of print]16(11):

Apoptotic Caspases Suppress Expression of Endogenous Retroviruses in HPV31+ Cells That Are Associated with Activation of an Innate Immune Response.

Caleb Studstill, Ning Huang, Shelby Sundstrom, Samantha Moscoso, Huirong Zhang, Blossom Damania, Cary Moody.

  Avoidance of an immune response is critical to completion of the human papillomavirus (HPV) life cycle, which occurs in the stratified epithelium and is linked to epithelial differentiation. We previously demonstrated that high-risk HPVs use apoptotic caspases to suppress an antiviral innate immune response during the productive phase of the life cycle. We found that caspase-8 and caspase-3 suppress a type I IFN-β and type III IFN-λ response by disabling the MDA5/MAVS double-stranded RNA (dsRNA) sensing pathway, indicating that immunogenic RNAs increase upon differentiation in HPV+ cells. In this study, we demonstrate that caspase inhibition results in aberrant transcription of a subset of endogenous retroviruses (ERVs) that have been shown to activate an IFN response through dsRNA-sensing pathways. We show that the increase in ERV transcription is accompanied by an enrichment in dsRNA formation. Additionally, we demonstrate that the robust increase in ERV expression requires activation of the JAK/STAT-signaling pathway, indicating that this subset of ERVs is IFN-inducible. Overall, these results suggest a model by which caspase activity blocks the reactivation of ERVs through the JAK/STAT pathway, protecting HPV+ cells from an increase in immunogenic dsRNAs that otherwise would trigger an IFN response that inhibits productive viral replication.

Keywords:  endogenous retrovirus; human papillomavirus; innate immunity; viral life cycle

DOI:  https://doi.org/10.3390/v16111695
Front Neurosci. 2024 ;18 1496142

Mutations in mitochondrial ATAD3 gene and disease, lessons from in vivo models.

Marcel Brügel, Ann-Sophie Kiesel, Tobias B Haack, Susana Peralta.

  Pathogenic variants in the ATAD3 gene cluster have been associated with different neurodevelopmental disorders showing clinical symptoms like global developmental delay, muscular hypotonia, cardiomyopathy, congenital cataracts, and cerebellar atrophy. ATAD3A encodes for a mitochondrial ATPase whose function is unclear and has been considered one of the five most common nuclear genes associated with mitochondrial diseases in childhood. However, the mechanism causing ATAD3-associated disorders is still unknown. In vivo models have been used to identify ATAD3 function. Here we summarize the features of mouse models with ATAD3 loss of function and Drosophila models overexpressing pathogenic ATAD3 variants. We discuss how these models have contributed to our understanding of ATAD3 function and the pathomechanism of the ATAD3-associated disease.

Keywords:  ATAD3; animal model; cholesterol; mitochondrial disease; mtDNA depletion and deletion; neurodegeneration

DOI:  https://doi.org/10.3389/fnins.2024.1496142
PLoS One. 2024 ;19(11): e0313000

Deep learning-enhanced automated mitochondrial segmentation in FIB-SEM images using an entropy-weighted ensemble approach.

Yubraj Gupta, Rainer Heintzmann, Carlos Costa, Rui Jesus, Eduardo Pinho.

Mitochondria are intracellular organelles that act as powerhouses by breaking down nutrition molecules to produce adenosine triphosphate (ATP) as cellular fuel. They have their own genetic material called mitochondrial DNA. Alterations in mitochondrial DNA can result in primary mitochondrial diseases, including neurodegenerative disorders. Early detection of these abnormalities is crucial in slowing disease progression. With recent advances in data acquisition techniques such as focused ion beam scanning electron microscopy, it has become feasible to capture large intracellular organelle volumes at data rates reaching 4Tb/minute, each containing numerous cells. However, manually segmenting large data volumes (gigapixels) can be time-consuming for pathologists. Therefore, there is an urgent need for automated tools that can efficiently segment mitochondria with minimal user intervention. Our article proposes an ensemble of two automatic segmentation pipelines to predict regions of interest specific to mitochondria. This architecture combines the predicted outputs from both pipelines using an ensemble learning-based entropy-weighted fusion technique. The methodology minimizes the impact of individual predictions and enhances the overall segmentation results. The performance of the segmentation task is evaluated using various metrics, ensuring the reliability of our results. We used four publicly available datasets to evaluate our proposed method's effectiveness. Our proposed fusion method has achieved a high score in terms of the mean Jaccard index and dice coefficient for all four datasets. For instance, in the UroCell dataset, our proposed fusion method achieved scores of 0.9644 for the mean Jaccard index and 0.9749 for the Dice coefficient. The mean error rate and pixel accuracy were 0.0062 and 0.9938, respectively. Later, we compared it with state-of-the-art methods like 2D and 3D CNN algorithms. Our ensemble approach shows promising segmentation efficiency with minimal intervention and can potentially aid in the early detection and mitigation of mitochondrial diseases.

DOI: https://doi.org/10.1371/journal.pone.0313000
bioRxiv. 2024 Nov 12. pii: 2024.11.12.623278. [Epub ahead of print]

Quantification of subcellular RNA localization through direct detection of RNA oxidation.

Hei-Yong G Lo, Raeann Goering, Agnese Kocere, Joelle Lo, Megan C Pockalny, Laura K White, Haydee Ramirez, Abraham Martinez, Seth Jacobson, Robert C Spitale, Chad G Pearson, Marino J E Resendiz, Christian Mosimann, J Matthew Taliaferro.

Across cell types and organisms, thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes, multiple proximity-based techniques have been developed in which RNAs near a localized bait protein are specifically labeled, facilitating their biotinylation and purification. However, these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations, we developed Oxidation-Induced Nucleotide Conversion sequencing (OINC-seq). In OINC-seq, RNAs near a genetically encoded, localized bait protein are specifically oxidized in a photo-controllable manner. These oxidation events are then directly detected and quantified using high-throughput sequencing and our software package, PIGPEN, without the need for biotin-mediated enrichment. We demonstrate that OINC-seq can induce and quantify RNA oxidation with high specificity in a dose- and light-dependent manner. We further show the spatial specificity of OINC-seq by using it to quantify subcellular transcriptomes associated with the cytoplasm, ER, nucleus, and the inner and outer membranes of mitochondria. Finally, using transgenic zebrafish, we demonstrate that OINC-seq allows proximity-mediated RNA labeling in live animals. In sum, OINC-seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems.

DOI: https://doi.org/10.1101/2024.11.12.623278
Aging Cell. 2024 Nov 28. e14440

Piezo1 exacerbates inflammation-induced cartilaginous endplate degeneration by activating mitochondrial fission via the Ca2+/CaMKII/Drp1 axis.

Zhidi Lin, Guangyu Xu, Xiao Lu, Hongli Wang, Feizhou Lu, Xinlei Xia, Jian Song, Jianyuan Jiang, Xiaosheng Ma, Fei Zou.

  Mitochondrial homeostasis plays a crucial role in degenerative joint diseases, including cartilaginous endplate (CEP) degeneration. To date, research into mitochondrial dynamics in IVDD is at an early stage. Since Piezo1 is a novel Ca2+-permeable channel, we asked whether Piezo1 could modulate mitochondrial fission through Ca2+ signalling during CEP degeneration. In vitro and in vivo models of inflammation-induced CEP degeneration were established with lipopolysaccharide (LPS). We found increased expression of Piezo1 in degenerated CEP tissues and LPS-treated CEP cells. The Piezo1 activator Yoda1 exacerbated CEP cell senescence and apoptosis by triggering Ca2+ influx. Yoda1 also induced mitochondrial fragmentation and dysfunction. In contrast, the Piezo1 inhibitor GsMTx4 exerted cytoprotective effects in LPS-treated CEP cells. Additionally, the CaMKII inhibitor KN-93 reversed Yoda1-induced mitochondrial fission and restored mitochondrial function. Mechanistically, the phosphorylation and mitochondrial translocation of Drp1 were regulated by the Ca2+/CaMKII signalling. The Drp1 inhibitor Mdivi-1 suppressed mitochondrial fission, then reduced mitochondrial dysfunction and CEP cell death. Moreover, knockdown of Piezo1 by siRNA hindered CaMKII and Drp1 activation, facilitating the redistribution of mitochondrial Drp1 to the cytosol in LPS-treated CEP cells. Piezo1 silencing improved mitochondrial morphology and function, thereby rescuing CEP cell senescence and apoptosis under inflammatory conditions. Finally, subendplate injection of GsMTx4 or AAV-shPiezo1 alleviated CEP degeneration in a rat model. Thus, Piezo1 may exacerbate inflammation-induced CEP degeneration by triggering mitochondrial fission and dysfunction via the Ca2+/CaMKII/Drp1 axis.

Keywords:  Drp1; Piezo1; apoptosis; cartilaginous endplate degeneration; mitochondrial fission; senescence

DOI:  https://doi.org/10.1111/acel.14440
Cell Metab. 2024 Nov 23. pii: S1550-4131(24)00417-0. [Epub ahead of print]

Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.

Gaia Gherardi, Anna Weiser, Flavien Bermont, Eugenia Migliavacca, Benjamin Brinon, Guillaume E Jacot, Aurélie Hermant, Mattia Sturlese, Leonardo Nogara, Filippo Vascon, Agnese De Mario, Andrea Mattarei, Emma Garratt, Mark Burton, Karen Lillycrop, Keith M Godfrey, Laura Cendron, Denis Barron, Stefano Moro, Bert Blaauw, Rosario Rizzuto, Jerome N Feige, Cristina Mammucari, Umberto De Marchi.

  Mitochondrial calcium (mtCa2+) uptake via the mitochondrial calcium uniporter (MCU) couples calcium homeostasis and energy metabolism. mtCa2+ uptake via MCU is rate-limiting for mitochondrial activation during muscle contraction, but its pathophysiological role and therapeutic application remain largely uncharacterized. By profiling human muscle biopsies, patient-derived myotubes, and preclinical models, we discovered a conserved downregulation of mitochondrial calcium uniporter regulator 1 (MCUR1) during skeletal muscle aging that associates with human sarcopenia and impairs mtCa2+ uptake and mitochondrial respiration. Through a screen of 5,000 bioactive molecules, we identify the natural polyphenol oleuropein as a specific MCU activator that stimulates mitochondrial respiration via mitochondrial calcium uptake 1 (MICU1) binding. Oleuropein activates mtCa2+ uptake and energy metabolism to enhance endurance and reduce fatigue in young and aged mice but not in muscle-specific MCU knockout (KO) mice. Our work demonstrates that impaired mtCa2+ uptake contributes to mitochondrial dysfunction during aging and establishes oleuropein as a novel food-derived molecule that specifically targets MCU to stimulate mitochondrial bioenergetics and muscle performance.

Keywords:  MCU; MCUR1; aging; calcium signaling; endurance; energy; fatigue; mitochondria; polyphenols; sarcopenia; skeletal muscle

DOI:  https://doi.org/10.1016/j.cmet.2024.10.021
Cell Stress. 2024 ;8 99-111

Neuroglobin-enriched secretome provides neuroprotection against hydrogen peroxide and mitochondrial toxin-induced cellular stress.

Giovanna Bastari, Virginia Solar Fernandez, Maurizio Muzzi, Sandra Moreno, Maria Marino, Marco Fiocchetti.

  Aberrant response to physiological cell stress is part of the mechanisms underlying the development of diverse human diseases, including neuropathologies. Neuroglobin (NGB), an intracellular monomeric globin, has gained attention for its role in endogenous stress response pathways in neuroprotection. To date, evidence supports the concept of NGB as an inducible protein, triggered by physiological and pathological stimuli via transcriptional and/or post-transcriptional mechanisms, offering cell-autonomous neuroprotective functions under various cellular stresses. Notably, recent evidence suggests the extracellular occurrence of NGB. We aimed to explore whether NGB redistribution in the cell microenvironment may serve in transmitting resilience capability in a model with neuronal characteristics. Results obtained in SH-SY5Y demonstrated that intracellular NGB upregulation is associated with the promotion of the extracellular release of the globin. Additionally, cell secretome from NGB-overexpressing cells, characterized by globin accumulation, exhibits protective effects against oxidative stress and mitochondrial toxicity, as evidenced by reduced apoptosis and preserved mitochondrial structure. These findings shed light on the potential significance of extracellular NGB as part of a common cell response to physiological and stress conditions and as a factor promoting cell resilience. Furthermore, the potential for neuroprotection of extracellular NGB paves the way for future therapeutic opportunities.

Keywords:  mitochondria; neurodegeneration; neuroglobin; neuronal stress; secretome

DOI:  https://doi.org/10.15698/cst2024.11.300
Nat Struct Mol Biol. 2024 Nov 28.

Structure and function of the human mitochondrial MRS2 channel.

Zhihui He, Yung-Chi Tu, Chen-Wei Tsai, Jonathan Mount, Jingying Zhang, Ming-Feng Tsai, Peng Yuan.

The human mitochondrial RNA splicing 2 protein (MRS2) has been implicated in Mg2+ transport across mitochondrial inner membranes, thus having an important role in Mg2+ homeostasis critical for mitochondrial integrity and function. However, the molecular mechanisms underlying its fundamental channel properties such as ion selectivity and regulation remain unclear. Here we present a structural and functional investigation of MRS2. Cryo-electron microscopy structures in various ionic conditions reveal a pentameric channel architecture and the molecular basis of ion permeation and potential regulation mechanisms. Electrophysiological analyses demonstrate that MRS2 is a Ca2+-regulated, nonselective channel permeable to Mg2+, Ca2+, Na+ and K+, which contrasts with its prokaryotic ortholog, CorA, operating as a Mg2+-gated Mg2+ channel. Moreover, a conserved arginine ring within the pore of MRS2 functions to restrict cation movements, thus preventing the channel from collapsing the proton motive force that drives mitochondrial adenosine triphosphate synthesis. Together, our results provide a molecular framework for further understanding MRS2 in mitochondrial function and disease.

DOI: https://doi.org/10.1038/s41594-024-01420-5